list index error while using Mordred

[vaibhavadixit]

description I am facing the following error trying to use Mordred in anaconda prompt. The module was working fine last week and I did generate expected ouput.csv files with descriptors, but it is now giving the error given below. The test job is also giving some errors (given below). Can you please take a look and suggest me how to fix these errors? Thank you and regards Dr. Vaibhav A. Dixit, Assistant Professor, Department of Pharmacy, ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄ Birla Institute of Technology and Sciences Pilani (BITS-Pilani), VidyaVihar Campus, street number 41, Pilani, 333031, Rajasthan. India Phone No. +91 1596 255652, Mob. No. +91-7709129400, Email: vaibhav.dixit@pilani.bits-pilani.ac.in, vaibhavadixit@gmail.com ​http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/ ORCID ID: https://orcid.org/0000-0003-4015-2941 http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra

minimal reproduction code

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environment

OS/distribution

windows Please fill me.

conda or pip

conda Please choose conda or pip.

python version

Python 3.6.7 |Anaconda custom (64-bit)| (default, Oct 28 2018, 19:44:12) [MSC v.1915 64 bit (AMD64)] on win32 Type "help", "copyright", "credits" or "license" for more information.

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python --version

library version

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(base) C:\Users\user\Vaibhav>python -m mordred -o output.csv CYP3A4-inhi-active-notactive.smi -3 -v Traceback (most recent call last): File "C:\Users\user\PyMOL\lib\runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "C:\Users\user\PyMOL\lib\runpy.py", line 85, in _run_code exec(code, run_globals) File "C:\Users\user\PyMOL\lib\site-packages\mordred__main.py", line 203, in main() File "C:\Users\user\PyMOL\lib\site-packages\mordred__main.py", line 197, in main descriptor=p.descriptor, with3D=p.with3D, verbosity=p.verbosity, File "C:\Users\user\PyMOL\lib\site-packages\mordred__main__.py", line 125, in main_process mols = list(mols) File "C:\Users\user\PyMOL\lib\site-packages\mordred\main.py", line 117, in mols = (m for i in input for m in parser(i)) File "C:\Users\user\PyMOL\lib\site-packages\mordred\main__.py", line 66, in auto_parser for m in r: File "C:\Users\user\PyMOL\lib\site-packages\mordred\main__.py", line 26, in smiles_parser smi = line[0] IndexError: list index out of range

Test jobs errors: (base) C:\Users\user\Vaibhav>python -m mordred.tests ...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................E.........................E............................................................................................................................. .........................................................................................................................................................................................................E....

ERROR: Failure: ModuleNotFoundError (No module named 'yaml')

Traceback (most recent call last): File "C:\Users\user\AppData\Roaming\Python\Python36\site-packages\nose\failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "C:\Users\user\AppData\Roaming\Python\Python36\site-packages\nose\loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "C:\Users\user\AppData\Roaming\Python\Python36\site-packages\nose\importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "C:\Users\user\AppData\Roaming\Python\Python36\site-packages\nose\importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "C:\Users\user\PyMOL\lib\imp.py", line 235, in load_module return load_source(name, filename, file) File "C:\Users\user\PyMOL\lib\imp.py", line 172, in load_source module = _load(spec) File "", line 684, in _load File "", line 665, in _load_unlocked File "", line 678, in exec_module File "", line 219, in _call_with_frames_removed File "C:\Users\user\PyMOL\lib\site-packages\mordred\tests\test_by_references.py", line 4, in import yaml ModuleNotFoundError: No module named 'yaml'

====================================================================== ERROR: Failure: ImportError (cannot import name 'AbstractMethodError')

Traceback (most recent call last): File "C:\Users\user\AppData\Roaming\Python\Python36\site-packages\nose\failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "C:\Users\user\AppData\Roaming\Python\Python36\site-packages\nose\loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "C:\Users\user\AppData\Roaming\Python\Python36\site-packages\nose\importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "C:\Users\user\AppData\Roaming\Python\Python36\site-packages\nose\importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "C:\Users\user\PyMOL\lib\imp.py", line 235, in load_module return load_source(name, filename, file) File "C:\Users\user\PyMOL\lib\imp.py", line 172, in load_source module = _load(spec) File "", line 684, in _load File "", line 665, in _load_unlocked File "", line 678, in exec_module File "", line 219, in _call_with_frames_removed File "C:\Users\user\PyMOL\lib\site-packages\mordred\tests\test_pandas.py", line 5, in from mordred._base.pandas_module import MordredDataFrame File "C:\Users\user\PyMOL\lib\site-packages\mordred_base\pandas_module.py", line 2, in from pandas import Series, DataFrame File "C:\Users\user\PyMOL\lib\site-packages\pandas__init.py", line 42, in from pandas.core.api import * File "C:\Users\user\PyMOL\lib\site-packages\pandas\core\api.py", line 10, in from pandas.core.groupby import Grouper File "C:\Users\user\PyMOL\lib\site-packages\pandas\core\groupby\init.py", line 2, in from pandas.core.groupby.groupby import ( File "C:\Users\user\PyMOL\lib\site-packages\pandas\core\groupby\groupby.py", line 48, in from pandas.core.arrays import ExtensionArray, Categorical File "C:\Users\user\PyMOL\lib\site-packages\pandas\core\arrays\init__.py", line 1, in from .base import ExtensionArray # noqa File "C:\Users\user\PyMOL\lib\site-packages\pandas\core\arrays\base.py", line 10, in from pandas.errors import AbstractMethodError ImportError: cannot import name 'AbstractMethodError'

====================================================================== ERROR: Failure: ImportError (cannot import name 'AbstractMethodError')

Traceback (most recent call last): File "C:\Users\user\AppData\Roaming\Python\Python36\site-packages\nose\failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "C:\Users\user\AppData\Roaming\Python\Python36\site-packages\nose\loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "C:\Users\user\AppData\Roaming\Python\Python36\site-packages\nose\importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "C:\Users\user\AppData\Roaming\Python\Python36\site-packages\nose\importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "C:\Users\user\PyMOL\lib\imp.py", line 235, in load_module return load_source(name, filename, file) File "C:\Users\user\PyMOL\lib\imp.py", line 172, in load_source module = _load(spec) File "", line 684, in _load File "", line 665, in _load_unlocked File "", line 678, in exec_module File "", line 219, in _call_with_frames_removed File "C:\Users\user\PyMOL\lib\site-packages\mordred_base\pandas_module.py", line 2, in from pandas import Series, DataFrame File "C:\Users\user\PyMOL\lib\site-packages\pandas__init.py", line 42, in from pandas.core.api import * File "C:\Users\user\PyMOL\lib\site-packages\pandas\core\api.py", line 10, in from pandas.core.groupby import Grouper File "C:\Users\user\PyMOL\lib\site-packages\pandas\core\groupby\init.py", line 2, in from pandas.core.groupby.groupby import ( File "C:\Users\user\PyMOL\lib\site-packages\pandas\core\groupby\groupby.py", line 48, in from pandas.core.arrays import ExtensionArray, Categorical File "C:\Users\user\PyMOL\lib\site-packages\pandas\core\arrays\init__.py", line 1, in from .base import ExtensionArray # noqa File "C:\Users\user\PyMOL\lib\site-packages\pandas\core\arrays\base.py", line 10, in from pandas.errors import AbstractMethodError ImportError: cannot import name 'AbstractMethodError'

---

Ran 61286 tests in 60.156s

FAILED (errors=3)

• conda

  conda list

  (base) C:\Users\user\Vaibhav>conda list

  packages in environment at C:\Users\user\PyMOL:

  #

  Name Version Build Channel

  anaconda custom py36h363777c_0 anyqt 0.0.10 py36_0 apbs 1.5 1 schrodinger asn1crypto 0.24.0 py36_0 babel 2.6.0 pypi_0 pypi base58 1.0.3 pypi_0 pypi blas 1.0 mkl bottleneck 1.2.1 py36h452e1ab_1 ca-certificates 2019.1.23 0 cachecontrol 0.12.5 pypi_0 pypi cairo 1.14.12 hf171d8a_3 certifi 2019.3.9 py36_0 cffi 1.11.5 py36h74b6da3_1 chardet 3.0.4 py36_1 cloudpickle 0.8.0 pypi_0 pypi conda 4.6.8 py36_0 conda-env 2.6.0 h36134e3_1 console_shortcut 0.1.1 h6bb2dd7_3 cryptography 2.3.1 py36h74b6da3_0 cycler 0.10.0 py36h009560c_0 decorator 4.3.2 py36_0 docutils 0.14 py36h6012d8f_0 entrypoints 0.3 py36_0 et-xmlfile 1.0.1 pypi_0 pypi fasttsne 0.2.13 py36h8c2d366_1 freemol 1.158 py36_1 schrodinger freetype 2.9.1 ha9979f8_1 gitdb2 2.0.5 pypi_0 pypi gitpython 2.1.11 pypi_0 pypi glew 2.0.0 0 schrodinger grep 0.3.2 pypi_0 pypi h2 2.6.2 pypi_0 pypi h5py 2.8.0 py36h3bdd7fb_2 hdf5 1.10.2 hac2f561_1 hpack 3.0.0 pypi_0 pypi hyper 0.7.0 pypi_0 pypi hyperframe 3.2.0 pypi_0 pypi icc_rt 2017.0.4 h97af966_0 icu 58.2 ha66f8fd_1 idna 2.8 py36_0 intel-openmp 2018.0.3 0 jdcal 1.4 pypi_0 pypi joblib 0.13.2 py36_0 jpeg 9b hb83a4c4_2 keyring 18.0.0 py36_0 keyrings.alt 3.1.1 py36_0 kiwisolver 1.0.1 py36h6538335_0 libboost 1.67.0 hd9e427e_4 libiconv 1.15 h1df5818_7 libpng 1.6.34 h79bbb47_0 libtiff 4.0.9 h36446d0_2 libxml2 2.9.8 hadb2253_1 linecache2 1.0.0 py36_0 llvmlite 0.27.0 py36ha925a31_0 loky 2.4.2 pypi_0 pypi makeportable 1.0 3 schrodinger matplotlib 2.2.2 py36had4c4a9_2 mengine 1 0 schrodinger menuinst 1.4.14 py36hfa6e2cd_0 mkl 2018.0.3 1 mkl_fft 1.0.6 py36hdbbee80_0 mkl_random 1.0.1 py36h77b88f5_1 mordred 1.1.1 py36h39e3cac_0 mordred-descriptor mordred-web 0.3.4 pypi_0 pypi mpeg_encode 1 0 schrodinger msgpack-python 0.5.6 py36he980bc4_1 mtz2ccp4_px 1.0 1 schrodinger networkx 2.2 py36_1 normalize 1.0.4 pypi_0 pypi numba 0.42.0 py36hf9181ef_0 numpy 1.15.4 py36ha559c80_0 numpy-base 1.15.4 py36h8128ebf_0 olefile 0.46 py36_0 openpyxl 2.6.0 pypi_0 pypi openssl 1.0.2r he774522_0 orange3 3.19.0 py36ha925a31_0 orange3-chemoinformatics 0.1.0 pypi_0 pypi pandas 0.22.0 pypi_0 pypi pdb2pqr 2.1.1 py36_1 schrodinger pillow 5.2.0 py36h08bbbbd_0 pip 19.0.3 pypi_0 pypi pixman 0.34.0 hcef7cb0_3 pmw 2.0.1 py36_2 schrodinger psutil 5.5.1 pypi_0 pypi py-boost 1.67.0 py36h8300f20_4 pycosat 0.6.3 py36hfa6e2cd_0 pycparser 2.19 py36_0 pydpi 1.0 pypi_0 pypi pymol 2.3.0 py36_0 schrodinger pymol-upgrade-helper 1.0 1 schrodinger pymol-web-examples 2.0 2 schrodinger pymol-web-legacy 2.0 py_1 schrodinger pyopenssl 19.0.0 py36_0 pyparsing 2.3.1 py36_0 pyqt 5.6.0 py36ha878b3d_6 pyqtgraph 0.10.0 py36h28b3542_3 pysocks 1.6.8 py36_0 python 3.6.7 h33f27b4_1 python-dateutil 2.7.5 py36_0 python-louvain 0.11 py36h28b3542_0 pytz 2018.9 py36_0 pywin32 223 py36hfa6e2cd_1 qt 5.6.2 vc14h6f8c307_12 rdkit 2018.09.2.0 py36h07f3614_1 rdkit requests 2.21.0 py36_0 richenum 1.2.1 pypi_0 pypi rigimol 1.3 2 schrodinger ruamel_yaml 0.15.46 py36hfa6e2cd_0 scikit-learn 0.20.2 pypi_0 pypi scipy 1.2.1 pypi_0 pypi serverfiles 0.3.0 py36_0 setuptools 40.7.3 py36_0 simplemmtf-python 0.2 0 schrodinger sip 4.18.1 py36h6538335_2 six 1.12.0 py36_0 sklearn 0.0 pypi_0 pypi smmap2 2.0.5 pypi_0 pypi sqlite 3.25.2 hfa6e2cd_0 tk 8.6.8 hfa6e2cd_0 tornado 5.1.1 py36hfa6e2cd_0 tqdm 4.31.1 py_0 traceback2 1.4.0 py36_0 unique 0.1 pypi_0 pypi unittest2 1.1.0 py36_0 urllib3 1.24.1 py36_0 vc 14.1 h0510ff6_4 vs2008_runtime 9.00.30729.5054 0 vs2013_runtime 12.0.21005 1 vs2015_runtime 14.15.26706 h3a45250_0 wheel 0.32.3 py36_0 win_inet_pton 1.0.1 py36_1 win_unicode_console 0.5 py36hcdbd4b5_0 wincertstore 0.2 py36h7fe50ca_0 xlrd 1.2.0 py36_0 xz 5.2.4 h2fa13f4_4 yaml 0.1.7 hc54c509_2 zlib 1.2.11 h8395fce_2

• pip

  python -m pip list
  python -c 'import rdkit; print("rdkit " + rdkit.__version__)'

  (base) C:\Users\user\Vaibhav> python -m pip list Package Version

  ---

  AnyQt 0.0.10 asn1crypto 0.24.0 Babel 2.6.0 backcall 0.1.0 base58 1.0.3 bleach 3.0.2 Bottleneck 1.2.1 CacheControl 0.12.5 certifi 2019.3.9 cffi 1.11.5 chardet 3.0.4 cloudpickle 0.8.0 colorama 0.4.0 conda 4.6.8 cryptography 2.3.1 cycler 0.10.0 decorator 4.3.0 defusedxml 0.5.0 docutils 0.14 entrypoints 0.2.3 et-xmlfile 1.0.1 fastTSNE 0.2.13 freemol 1.158 gitdb2 2.0.5 GitPython 2.1.11 grep 0.3.2 h2 2.6.2 h5py 2.8.0 hpack 3.0.0 hyper 0.7.0 hyperframe 3.2.0 idna 2.8 ipykernel 5.1.0 ipython 7.1.1 ipython-genutils 0.2.0 ipywidgets 7.4.2 jdcal 1.4 jedi 0.13.1 Jinja2 2.10 joblib 0.13.2 jsonschema 2.6.0 jupyter 1.0.0 jupyter-client 5.2.3 jupyter-console 6.0.0 jupyter-core 4.4.0 keyring 18.0.0 keyrings.alt 3.1.1 kiwisolver 1.0.1 linecache2 1.0.0 llvmlite 0.27.0 loky 2.4.2 MarkupSafe 1.1.0 matplotlib 3.0.2 menuinst 1.4.14 mistune 0.8.4 mkl-fft 1.0.6 mkl-random 1.0.1 mordred 1.1.1 mordred-web 0.3.4 mpmath 1.0.0 msgpack 0.5.6 nbconvert 5.4.0 nbformat 4.4.0 networkx 2.2 normalize 1.0.4 nose 1.3.7 notebook 5.7.2 numba 0.42.0 numpy 1.15.4 olefile 0.46 openpyxl 2.6.0 Orange3 3.19.0 Orange3-Chemoinformatics 0.1.0 pandas 0.23.4 pandocfilters 1.4.2 parso 0.3.1 pdb2pqr-minimal 0.0.0 pickleshare 0.7.5 Pillow 5.2.0 pip 19.0.3 prometheus-client 0.4.2 prompt-toolkit 2.0.7 psutil 5.5.1 pycosat 0.6.3 pycparser 2.19 pydpi 1.0 Pygments 2.2.0 pymol 2.3.0 pyOpenSSL 19.0.0 pyparsing 2.3.0 pyqtgraph 0.10.0 PySocks 1.6.8 python-dateutil 2.7.5 python-louvain 0.11 pytz 2018.7 pywin32 223 pywinpty 0.5.4 pyzmq 17.1.2 qtconsole 4.4.3 requests 2.21.0 richenum 1.2.1 ruamel-yaml 0.15.46 scikit-learn 0.20.2 scipy 1.1.0 Send2Trash 1.5.0 serverfiles 0.3.0 setuptools 40.7.3 six 1.11.0 sklearn 0.0 smmap2 2.0.5 sympy 1.3 terminado 0.8.1 testpath 0.4.2 tornado 5.1.1 tqdm 4.31.1 traceback2 1.4.0 traitlets 4.3.2 unique 0.1 unittest2 1.1.0 urllib3 1.24.1 wcwidth 0.1.7 webencodings 0.5.1 wheel 0.32.3 widgetsnbextension 3.4.2 win-inet-pton 1.0.1 win-unicode-console 0.5 wincertstore 0.2 xlrd 1.2.0

(base) C:\Users\user\Vaibhav>python Python 3.6.7 |Anaconda custom (64-bit)| (default, Oct 28 2018, 19:44:12) [MSC v.1915 64 bit (AMD64)] on win32 Type "help", "copyright", "credits" or "license" for more information.

import rdkit print("rdkit" + rdkit.version) rdkit2018.09.2

[philopon]

I appreciate your thoughtful report.

It seems loads pandas included in PyMOL instead of conda package. Please check your PATH environment variable?

python -c 'import sys; [print(p) for p in sys.path]'

And, please check PYTHONPATH environment variable when C:\Users\user\PyMOL\lib\site-packages is found.

python -c 'import os; print(os.environ.get("PYTHONPATH"))'

Thanks,

[porteusconf]

You are missing pyyaml I also had similar nose and yaml errors fixed in miniconda3 by conda install nose pyyaml